Question: Newbie- Graphing genes along genome with multiple tracks
0
gravatar for berrysweetpie
5.4 years ago by
United States
berrysweetpie0 wrote:

I am new at using R for bioinformatics and have to generate graphics for the genome of yeast, with color coded genes and exon segments. The data I will be utilzing involves the start and end locations of these segments.

I also need to include an additional track with statistical analysis plots for each gene that are aligned vertically.

I am lost as to how to start on this, which packages to use for my preferred output, etc. and would appreciate any help on this.

sequencing gene R genome • 1.5k views
ADD COMMENTlink modified 5.4 years ago by bbio90 • written 5.4 years ago by berrysweetpie0

This is a very specific request; you'll have to provide us with example data and a closely related example of what you want the output to look like (i.e. from another study or source as an example).

Tentatively though, I think this is the type of effort for which you might want to use a GUI-based program like Geneious (requires a license) or Galaxy (free).

ADD REPLYlink written 5.4 years ago by Steven Lakin1.5k

Thank you for the quick response. The data is pretty simple, it involves the start and end sites for particular genes for yeast.

eg.

Gene Name   Strand     T3           T5

A                    -           10000     10020

A                    -           10005     10025

B                    +          11400     11500

If that makes any sense. The output should look something along the lines of this (with an additional track) though I am unsure what package was used to create it. I apologize if I am unclear

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by berrysweetpie0
1
gravatar for bbio
5.4 years ago by
bbio90
United Kingdom
bbio90 wrote:

I have used ggbio (and in particular ggbio's tracks() function) before for something very similar this. It has some bugs but in general it works quite well!

Example:

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by bbio90

This may work out for me! Do you know if the graphic output I pasted above was developed with this package?

ADD REPLYlink written 5.4 years ago by berrysweetpie0

No, that graphic looks like it was made with some other tool. If you need to get something very close to the example you posted you could try drawing your own shapes using ggplot's geom_rect() and so on, but this would definitely be a bit more complicated.

ADD REPLYlink written 5.4 years ago by bbio90
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